bioMatrixLegend: Plot Legend on caOmicsV bioMatrix Layout

In caOmicsV: Visualization of multi-dimentional cancer genomics data

Description

Draw legend including of heatmap color scale and data categories. Graphic device must be initialized first.

Usage

    bioMatrixLegend(heatmapNames=NULL, categoryNames=NULL, binaryNames=NULL, 
            heatmapMin=-3, heatmapMax=3, colorType="BlueWhiteRed")

Arguments

heatmapNames	character vector of length 2, name(s) of dataset for heatmap, e.g., "RNASeq" and/or "miRNASeq"
categoryNames	character vector of length 2 or more, names of categories, e.g., "Methylation High", "Methylation Low", ...
binaryNames	character vector of length 2 , names of binary data, e.g., "DNA Amplification" and "DNA Deletion".
heatmapMin	numeric, minimum values of heatmap plot data, default -3 (z-scores)
heatmapMax	numeric, maximum values of heatmap plot data, default 3 (z-scores)
colorType	characte veector, one of "BlueWhiteRed", "GreenWhiteRed", "GreenYellowRed", "GreenBlackRed" , or "YellowToRed"

Details

This function will plot legend on the bottom of matrix layout if any argument is defined. The order of legend items (from left to right) is heatmap color scale followed by colored boxes for category data legend then colored points for binary data legend.

Value

None

Author(s)

Henry Zhang

Examples

    data(biomatrixPlotDemoData)
    plotBioMatrix(biomatrixPlotDemoData, summaryType="text")
    bioMatrixLegend(heatmapNames=c("RNASeq", "miRNASeq"), 
        categoryNames=c("Methyl H", "Methyl L"), 
        binaryNames=c("CN LOSS", "CN Gain"),   
        colorType="BlueWhiteRed")

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: bc3net
Loading required package: c3net
Loading required package: infotheo
Loading required package: Matrix
Loading required package: lattice

caOmicsV documentation built on Nov. 8, 2020, 8:23 p.m.